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In the early 2330s the Prophets brought about the existence of Benjamin Sisko by possessing a woman named Sarah and having her bring about a child with Joseph Sisko. The resulting offspring was the pre-ordained Emissary of the Prophets.

In "Sacrifice of Angels", Sisko says to the Prophets, "You've sent the Bajorans orbs and Emissaries." This is the only reference to additional Emissaries, but Sisko may have been referring to Akorem Laan.

The ancient texts concerning the Emissary said that the Prophets would "call him to them" and that they would "give him back his life." In 2369, KaiOpaka told Commander Benjamin Sisko after his arrival at Deep Space 9 that he was to be the Emissary, after reading his pagh. Opaka told Sisko that he must find the Celestial Temple, and warn the Prophets about the Cardassians. Shortly after, Sisko fulfilled the prophecies and became the Emissary by discovering the Bajoran wormhole and making contact with the beings within. During this contact, the Prophets helped him recover from the loss of his wife Jennifer Sisko at the Battle of Wolf 359, essentially "giving him back his life". (DS9: "Emissary")

As the Emissary, Sisko gained some much-needed legitimacy in his assignment to prepare Bajor for Federation membership. Although he was at first uncomfortable with being revered as a religious icon, he felt obliged to respect the Bajorans' beliefs, as did Starfleet. However, some Bajorans doubted the Prophets' choosing of a Human as the Emissary, in particular Kai Winn Adami, who resented the fact that she had to share the leadership of the Bajoran faith with an outsider and non-believer. She and Sisko would have an adversarial relationship, although she eventually begrudgingly admitted that he was the true Emissary. (DS9: "In the Hands of the Prophets", "Rapture")

Akorem Laan in 2372

For a brief time in 2372, Sisko willingly stepped aside when Akorem Laan emerged from the wormhole, having been transported two centuries into the future by the Prophets, and claimed himself to be the Emissary. His claim was supported by Kai Winn, as Akorem was a native Bajoran and shared her orthodox beliefs. However, Akorem called for the reinstatement of the D'jarra caste system, which would have voided Bajor's application for Federation membership. An orb shadow experience and increased violence following Akorem's reforms prompted Sisko to challenge Akorem's claim to the title of Emissary. The two traveled into the wormhole, where the Prophets told them that "the Sisko" was their chosen Emissary, and that they had sent Akorem into the future to remind him of that fact. (DS9: "Accession")

The role of Emissary took on a new, more crucial light in 2373, after Sisko received a series of pagh'tem'far, which allowed him to rediscover the lost Bajoran city of B'hala. These visions also led him to warn the Bajorans against accepting Federation membership, advice which would prove prophetic later that year when Bajor was spared from a Dominion invasion. The unearthing of B'hala, a year later, would yield an ancient stone tablet, bearing the inscription "Welcome Emissary." When Sisko approached the tablet, he received a vision which initiated the Reckoning, a cosmic duel between a Prophet and the Pah-wraithKosst Amojan. The Emissary's purpose was to initiate this battle, as Sisko did when he shattered the tablet on Deep Space 9 (the "Gateway to the Celestial Temple") and released the beings inside. Sisko was willing to see the battle through to the end, but it was interrupted by Kai Winn. (DS9: "Rapture", "The Reckoning")

The next phase of the Emissary's path took place at the end of 2374, when the wormhole disappeared after Dukat released a Pah-wraith into the Orb of Contemplation. Promising to learn what had happened to them, Sisko returned to Earth and received a number of visions, leading him to find the Orb of the Emissary on the planet Tyree. The Orb contained the Prophet who had once inhabited the body of Sarah Sisko, Benjamin Sisko's natural mother. From her, Sisko learned that his birth and role as Emissary had been pre-ordained by the Prophets. When Sisko opened the Orb, the Prophet was released back into the Celestial Temple, where she cast out the malevolent being. (DS9: "Tears of the Prophets", "Image in the Sand", "Shadows and Symbols")

Sisko fulfills his role as the Emissary

The Emissary's last and most difficult task came at the end of 2375. Dukat, who had become the antithesis to Sisko through his connection with the Pah-wraiths, planned to release them from their prison inside the Fire Caves, an event which would unleash a new era of destruction. Disguising himself as a Bajoran named Anjohl Tennan, Dukat convinced Kai Winn to turn away from the Prophets and use her authority as kai to obtain the Book of the Kosst Amojan, the key to opening the Pah-wraiths' prison. Together, the two of them nearly succeeded, and the Pah-wraiths selected Dukat as their Emissary. However, Sisko was able to destroy the book by plunging it, himself, and Dukat into the flames, thus forever imprisoning the Pah-wraiths. As he was falling through the cave, Sisko was taken into the Celestial Temple to join the Prophets. The Emissary's task had been completed, though Sisko's own destiny was far from over. (DS9: "Penumbra", "'Til Death Do Us Part", "Strange Bedfellows", "The Changing Face of Evil", "What You Leave Behind")

In "Sacrifice of Angels", the Dominion had a fleet waiting to conquer the Alpha Quadrant on the other side of the wormhole, and Benjamin was ready to sacrifice his life and those of the crew aboard the USS Defiant, but the Prophets stopped him. They forbade him from ending "the game", as they called corporeal existence, so he tried to convince them to destroy the ships:

"I don't want to see Bajor destroyed and neither do you. And we all know that's exactly what's going to happen if the Dominion takes over the Alpha Quadrant. You say you don't want me to sacrifice my life – fine, neither do I. You want to be gods – then be gods. I need a miracle. Bajor needs a miracle. Stop those ships!"

Benjamin says goodbye to Kasidy

The Prophets complied with his request, but they observed that Benjamin was trying to "control the game" and said a penance must be exacted. This penance came in the form of his departure from the corporeal world when he entered the Celestial Temple at the end of "What You Leave Behind".

Later, when the Prophets warned Sisko that marrying Kasidy would bring him "nothing but sorrow" in "'Til Death Do Us Part", he ignored their warning. They nonetheless allowed him to marry, and while Kasidy feared the Prophets were referring to her baby, the sorrow was that which Benjamin's departure would cause. These events were not directly tied together until the DS9 relaunch novels, although several fan theories existed.

In the Millennium trilogy, the opening of a second wormhole (β) results in the creation of an alternate timeline where Weyoun is appointed the Emissary of the "True" Prophets (β), and Sisko is seen as the Emissary of the "false" Prophets. This timeline was averted and Weyoun defeated, though Sisko was introduced during those events to a more secretive Bajoran religious sect which possessed prophecies regarding the Emissary that were unknown to the general Bajoran public, and which reveal that, although Sisko is not the Emissary, a Sisko will be the Emissary. Specifically, the true Emissary is the daughter of Sisko and Kasidy Yates, who, in an epilogue set after Sisko has joined the Prophets, has become regarded as the "Child of Bajor", to whom even the Kai would bow. This novel also elaborates on Sisko's opinion of his status as the Emissary, with Sisko stating that he accepts that the beings who live in the Celestial Temple are powerful, mysterious creatures who acknowledge him as the Bajoran Emissary, but he has no fixed ideas about the implications of that title beyond the obvious details such as his role in Bajoran religion.

In the novel Fearful Symmetry, set after the events of "What You Leave Behind", Sisko has an Orb experience while using the Orb of Souls (β), in which he meets with seven other individuals named Benjamin Sisko, each from a different universe. It is revealed that Benjamin Sisko is always born by the Prophets' design and is specifically meant to become the Emissary in every universe.